5YTE

Large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with with natural dT:dATP base pair

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7	293.15	0.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.169	α = 90
b = 109.169	β = 90
c = 91.003	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2016-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.9793	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.21	94.54	99.9	21.72	7.6		30234

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.21	2.25

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4DFK	2.21	94.54	30234	1602	99.92	0.18713	0.18432	0.23787	RANDOM	49.112

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.56	0.28		0.56		-1.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.94
r_dihedral_angle_4_deg	16.14
r_dihedral_angle_3_deg	15.942
r_dihedral_angle_1_deg	8.959
r_long_range_B_refined	3.19
r_long_range_B_other	3.19
r_angle_refined_deg	1.486
r_scangle_other	1.472
r_mcangle_it	1.224
r_mcangle_other	1.224
r_angle_other_deg	1.137
r_scbond_it	0.888
r_scbond_other	0.888
r_mcbond_it	0.747
r_mcbond_other	0.744
r_chiral_restr	0.09
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4282
Nucleic Acid Atoms	568
Solvent Atoms	290
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
PHASER	phasing